2. http://cs273a.stanford.edu [Bejerano Fall10/11] 1 Primer, Friday 10am, Beckman B-302 Ex. 1 is coming.

3. http://cs273a.stanford.edu [Bejerano Fall10/11] 2 Lecture 4 Our place in the tree of life Genome Size Genome Content: Repetitive Sequences Genes

4. http://cs273a.stanford.edu [Bejerano Fall10/11] 3 Our Place in the Tree of Life [Human Molecular Genetics, 3rd Edition]  you are here

5. http://cs273a.stanford.edu [Bejerano Fall10/11] 4 Metazoans (multi-cellular organisms) [Human Molecular Genetics, 3rd Edition]  you are here

6. http://cs273a.stanford.edu [Bejerano Fall10/11] 5 Vertebrates [Human Molecular Genetics, 3rd Edition]  you are here, Opossum, Lizard, Stickleback

7. Figure from Ryan Gregory (2005) INTERSPECIES VARIATION IN GENOME SIZE WITHIN VARIOUS GROUPS OF ORGANISMS 6http://cs273a.stanford.edu [Bejerano Fall10/11]

8. 7 Meet Your Genome Continues [Human Molecular Genetics, 3rd Edition]

9. http://cs273a.stanford.edu [Bejerano Fall10/11] 8

10. 9 Repeats / obile Elements ("selfish DNA") Human Genome: 3*10 9 letters 1.5% known function >50% junk

11. http://cs273a.stanford.edu [Bejerano Fall10/11] 10 [Adapted from Lunter]

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14. TE composition and assortment vary among eukaryotic genomes 20% 40% 60% 80% 100% Slime mold Budding yeast Fission yeast NeurosporaArabidopsis Rice Nematode Drosophila Mosquito Fugu Mouse Human DNA transposons LTR Retro. Non-LTR Retro. Feschotte & Pritham 2006 13http://cs273a.stanford.edu [Bejerano Fall09/10]

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21. http://cs273a.stanford.edu [Bejerano Fall10/11] 20 Assemby Challenges

22. http://cs273a.stanford.edu [Bejerano Fall10/11] 21 Inferring Phylogeny Using Repeats [Nishihara et al, 2006]

23. http://cs273a.stanford.edu [Bejerano Fall10/11] 22 Functional elements from obile Elements [Yass is a small town in New South Wales, Australia.] Co-option event, probably due to favorable genomic context [Bejerano et al., Nature 2006]

24. The amount of TE correlate positively with genome size Plasmodium Slime mold Budding yeast Fission yeast Neurospora Arabidopsis Brassica Rice Maize Nematode Drosophila Mosquito Sea squirt Zebrafish Fugu Mouse Human 0 500 1000 1500 2000 2500 3000 Genomic DNA TE DNA Protein-coding DNA Mb Feschotte & Pritham 2006 23http://cs273a.stanford.edu [Bejerano Fall09/10]

25. TEs Protein-coding genes The proportion of protein-coding genes decreases with genome size, while the proportion of TEs increases with genome size Gregory, Nat Rev Genet 2005 24

26. http://cs273a.stanford.edu [Bejerano Fall10/11] 25 Genome Size Variability 1pg = 978 Mb

27. http://cs273a.stanford.edu [Bejerano Fall10/11] 26 Simple Repeats Every possible motif of mono-, di, tri- and tetranucleotide repeats is vastly overrepresented in the human genome. These are called microsatellites, Longer repeating units are called minisatellites, The real long ones are called satellites. Highly polymorphic in the human population. Highly heterozygous in a single individual. As a result microsatellites are used in paternity testing, forensics, and the inference of demographic processes. There is no clear definition of how many repetitions make a simple repeat, nor how imperfect the different copies can be. Highly variable between genomes: e.g., using the same search criteria the mouse & rat genomes have 2-3 times more microsatellites than the human genome. They’re also longer in mouse & rat.

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31. Restriction enzymes recognize and make a cut within specific palindromic sequences, known as restriction sites, in the DNA. This is usually a 4- or 6 base pair sequence. blunt end sticky end 30 http://cs273a.stanford.edu [Bejerano Fall10/11]

32. DNA Fingerprint Basics DNA fragments of different size will be produced by a restriction enzyme that cuts at the points shown by the arrows. 31

33. DNA fragments are then separated based on size using gel electrophoresis. 32

34. DNA Fingerprinting can be used in paternity testing or murder cases. 33

35. http://cs273a.stanford.edu [Bejerano Fall10/11] 34

36. http://cs273a.stanford.edu [Bejerano Fall10/11] 35 From an evolutionary point of view transposons and simple repeats are very different. Different instances of the same transposon share common ancestry (but not necessarily a direct common progenitor). Different instances of the same simple repeat most often do not.

37. http://cs273a.stanford.edu [Bejerano Fall10/11] 36 The Gene-ome makes < 2% of the H.G. [Human Molecular Genetics, 3rd Edition]

38. 37 Gene Structure Signal – a string of DNA recognized by the cellular machinery http://cs273a.stanford.edu [Bejerano Fall10/11]

39. Gene Processing Eukaryotic Gene Structure 38 http://cs273a.stanford.edu [Bejerano Fall10/11]

40. 39 Gene Finding – The Practice Challenge: “The genes, the whole genes, and nothing but the genes” Problems: spliced ESTs  legitimate gene isoform? predicting gene isoforms tissue/condition-specific genes / gene isoforms single exon genes pseudogenes Practice:

41. http://cs273a.stanford.edu [Bejerano Fall10/11] 40 Evolution of Gene Finding Tools etc

42. http://cs273a.stanford.edu [Bejerano Fall10/11] 41 The Human Gene Set [HGC, 2001]

43. http://cs273a.stanford.edu [Bejerano Fall10/11] 42 [Celera, 2001]

44. http://cs273a.stanford.edu [Bejerano Fall10/11] 43 wrong!

45. http://cs273a.stanford.edu [Bejerano Fall10/11] 44 Signal Transduction

46. http://cs273a.stanford.edu [Bejerano Fall10/11] 45 Ancient Origins of Important Gene Families

47. 46 Multigene families due to:  Single gene duplication  Segment duplication: Tandem duplication or duplication transposition  a b c d e f g  a b c d e f b c d g  Horizontal gene transfer  Genome-wide doubling event

48. http://cs273a.stanford.edu [Bejerano Fall10/11] 47 Horizontal Gene Transfer

49. http://cs273a.stanford.edu [Bejerano Fall10/11] 48 Horizontal Gene Transfer in the H.G. [HGC, 2001] …

50. http://cs273a.stanford.edu [Bejerano Fall10/11] 49 Or is it? [Kurland et al., 2003]

51. http://cs273a.stanford.edu [Bejerano Fall10/11] 50 HGT between fish & their parasites

52. http://cs273a.stanford.edu [Bejerano Fall10/11] 51 Retroposed Genes and Pseudogenes